Variant report

Variant	rs58653169
Chromosome Location	chr15:99684931-99684932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99679173..99681039-chr15:99683301..99685426,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNM-2	chr15:99684622-99685575	ENSG00000261616.1

Variant related genes	Relation type
ENSG00000103852	Chromatin interaction
ENSG00000261616	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12439819	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440477	0.96[ASN][1000 genomes]
rs12440640	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12440982	0.96[ASN][1000 genomes]
rs12442235	0.99[ASN][1000 genomes]
rs1612365	0.82[ASN][1000 genomes]
rs1670229	0.80[ASN][1000 genomes]
rs1876741	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006670	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290352	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2861371	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134586	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3134587	0.82[ASN][1000 genomes]
rs3743242	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4965215	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4965216	0.93[ASN][1000 genomes]
rs4965446	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4965448	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4965451	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58627039	1.00[ASN][1000 genomes]
rs60513984	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73480175	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73480191	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:99665000-99714200	Weak transcription	NHEK	skin
3	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
5	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
6	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
7	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:99676200-99696200	Weak transcription	NH-A	brain
10	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
11	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
12	chr15:99676400-99690200	Weak transcription	HSMM	muscle
13	chr15:99676800-99694400	Weak transcription	HUVEC	blood vessel
14	chr15:99677600-99695200	Weak transcription	Hela-S3	cervix
15	chr15:99677800-99696200	Weak transcription	HMEC	breast
16	chr15:99678000-99687800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:99678200-99689000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:99678200-99696400	Weak transcription	Placenta	Placenta
19	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:99678400-99689200	Weak transcription	Right Ventricle	heart
21	chr15:99679400-99689600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:99679600-99688600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:99679600-99689200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:99679800-99685400	Weak transcription	Gastric	stomach
25	chr15:99679800-99685800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:99679800-99687800	Weak transcription	Dnd41	blood
27	chr15:99679800-99688800	Weak transcription	Fetal Intestine Large	intestine
28	chr15:99679800-99689000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:99679800-99689000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:99679800-99689200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:99679800-99689200	Weak transcription	Spleen	Spleen
32	chr15:99679800-99689200	Weak transcription	A549	lung
33	chr15:99679800-99696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:99679800-99696200	Weak transcription	Esophagus	oesophagus
35	chr15:99680200-99687800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr15:99681800-99685000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr15:99681800-99690200	Enhancers	Colon Smooth Muscle	Colon
38	chr15:99682000-99685200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr15:99682200-99685600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:99682200-99687000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr15:99682200-99687000	Enhancers	Rectal Smooth Muscle	rectum
42	chr15:99682200-99687400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:99682600-99685000	Enhancers	NHDF-Ad	bronchial
44	chr15:99682600-99689200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:99682800-99685000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:99683000-99685000	Enhancers	Liver	Liver
47	chr15:99683000-99686400	Enhancers	Stomach Smooth Muscle	stomach
48	chr15:99683400-99688800	Weak transcription	Brain Substantia Nigra	brain
49	chr15:99683600-99685000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:99683800-99685400	Enhancers	Duodenum Smooth Muscle	Duodenum

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